His writings include an introduction to Henry Merritt: Art Criticism and Romance, published in 1879 and Churches about Queen Victoria Street, a portfolio published in 1871, Victorian art and originality for the British Architect published in 1887, and The architecture of Queen Victoria's reign for the Art Journal, published in 1887. A Quiet Corner of England was published in 1875 after being circulated as a portfolio and a work regarding his mother-in-law, Adelaide Drummond, A Retrospect and Memoir, was published in 1915. Champneys' correspondence has been preserved in the General Collection of the Beinecke Rare Book and Manuscript Library.

His Cambridge works include the Archaeological Museum (1883), now Peterhouse Theatre, the Divinity and Literary School and Newnham College (between 1875 and 1910), for which he is credited for bringing a 'touch of lightness' to the college and is acknowledged for his attention to both construction details, and to cost.

Churches by Champneys include his father's parish church, St Luke's, Kentish Town (1867–1870), the sailors' church of St Mary Star of the Sea, Hastings (1878), and St Chad, Slindon, Staffordshire (1894). In 1898 he added a porch to St Mary, Manchester, where he was surveyor, and between 1902 and 1903, a south annexe. His home, Hall Oak, in Frognal, Hampstead was also one of his works.